seremi documentationΒΆ
pip install seremi
Read SER & EMI microscope images and metadata. These image files come from FEI TIA (Tecnai Imaging and Analysis) microscope software, originally created by Emispec.
# Example how to read metadata from EMI and frame content from SER
from argparse import ArgumentParser
from seremi import EMIFile, SERFile
import numpy as np
parser = ArgumentParser()
parser.add_argument('--ser', required=True, help='path to SER file, such as movie_1.ser')
parser.add_argument('--emi', required=True, help='path to EMI file, such as movie.emi')
args = parser.parse_args()
with SERFile(args.ser) as ser, EMIFile(args.emi) as emi:
# EMI contains detailed metadata, mostly in info_dict
voltage = emi.info_dict['ObjectInfo']['ExperimentalConditions']['MicroscopeConditions']['AcceleratingVoltage']
print(f'voltage={voltage}')
# read image content from SER
for i in range(ser.num_frames):
frame = ser.read_frame(i) # numpy array
print(f'frame {i} average: {np.mean(frame)}') # do something with the frame content
# EMI file contains the last frame of the SER
assert np.array_equal(emi.read_frame(), ser.read_last_frame())